Width test

Mermaid Bay

#devtools::install_github("marine-ecologist/coralseed",  lib = "/Users/rof011/coralseed")
#devtools::install("/Users/rof011/coralseed")

library(coralseed)
library(tidyverse)
library(sf)
library(tmap)
library(widgetframe)

seascape <- seascape_probability(reefoutline=reef_map, habitat=benthic_map)

palfrey09 <- "/Users/rof011/Library/CloudStorage/OneDrive-CSIRO/Data - SeaSims/conniemodels/Dispersal_SettlementRate/lizard_del_14_1512_sim1/lizard_del_14_1512_sim1/plots/day_12036/run_day_12036_lizard_del_14_1512_sim1_18.json"

particles <- seed_particles(input=palfrey09, seascape=seascape, 
                            competency.function = "exponential", 
                            limit.time = 720, simulate.mortality = "typeI", 
                            simulate.mortality.n = 0.1, probability="additive",
                            return.plot=FALSE, silent=TRUE)

settlers <-  settle_particles(particles, probability="additive", silent=TRUE)

interim code

seed_particles <- particles
settle_particles <- settlers
seascape_probability <- seascape
restoration.plot <- c(100,100)

particletracks <- seed_particles |> particles_to_tracks()
settler_density <- settle_particles |> settlement_density()
restoration_plot <- seed_particles |> set_restoration_plot(restoration.plot[1], restoration.plot[2])
#spatial_boundary <- seed_particles |> set_buffer(1)

settler_paths <- settle_particles$paths

map output

tmap::tmap_mode(mode = "view")

## tmap mode set to interactive viewing

tmp <- tmap::tmap_options(check.and.fix = TRUE) +
  
  tmap::tm_tiles("Esri.WorldImagery", group = "<b> [Seascape]</b> satellite map", alpha = 0.85) +
  tmap::tm_tiles("Esri.WorldTopoMap", group = "<b> [Seascape]</b> base map", alpha = 0.85) +

  # seascape habitats
  tmap::tm_shape(seascape_probability |> sf::st_make_valid(), name = "<b> [Seascape]</b> habitats") +
  tmap::tm_borders(col = "black", lwd = 0.2) +
  tmap::tm_fill("class",
    name = "Benthic habitats", alpha = 0.6,
    palette = c(
      "Plateau" = "cornsilk2",
      "Back Reef Slope" = "darkcyan",
      "Reef Slope" = "darkseagreen4",
      "Sheltered Reef Slope" = "darkslategrey",
      "Inner Reef Flat" = "darkgoldenrod4",
      "Outer Reef Flat" = "darkgoldenrod2",
      "Reef Crest" = "coral3"))  +

  # seascape probability  
  tmap::tm_shape(seascape_probability |> sf::st_make_valid(), name = "<b> [Seascape]</b> probability") +
  tmap::tm_fill("settlement_probability", id = "P settlement", alpha = 0.6) +
  tmap::tm_borders(col = "black", lwd = 0.2) +

  # particle tracks
  tmap::tm_shape(particletracks, name = "<b> [Particles]</b> competency") +
   tmap::tm_lines("competency", lwd = 0.8, palette = c("lightblue", "cadetblue4")) +
  # # 
  # # settlement paths
  tmap::tm_shape(settler_paths |> sf::st_make_valid(),  id="id", name = "<b> [Settlers]</b> pre-settlement tracks") +
  tmap::tm_lines(lwd = 0.8, col = "darkgrey") #+
  # 
  # # settlers
  # tmap::tm_shape(settle_particles$points, id="dispersaltime", name = "<b> [Settlers]</b> post-settlement location") +
  # tmap::tm_dots(col = "aquamarine3")  +
  # 
  # # settlement area
  # tmap::tm_shape(settler_density$area, id="area", name = "<b> [Settlers]</b> post-settlement area") +
  # tmap::tm_fill("polygons", col = "indianred4",  alpha = 0.6) +
  # tmap::tm_borders(lwd = 0, col = "black") +
  # 
  # # settlement grid
  # tmap::tm_shape(settler_density$density, name = "<b> [Stats]</b> spatial grid") +
  # tmap::tm_borders(lwd = 0.5, col = "black") +
  # 
  # # settlement count
  # tmap::tm_shape(settler_density$count, name = "<b> [Stats]</b> settlement count") +
  # tmap::tm_fill("count", colorNA = "transparent", name = "Settlement density", palette = "plasma", alpha = 0.6) +
  # tmap::tm_borders(lwd = 0, col = "black") +
  # 
  # # settlement density
  # tmap::tm_shape(settler_density$density, name = "<b> [Stats]</b> settlement density") +
  # tmap::tm_fill("density", colorNA = "transparent", name = "Settlement density", palette = "magma", alpha = 0.6) +
  # tmap::tm_borders(lwd = 0, col = "black") +
  # 
  # # restoration plot
  # tmap::tm_shape(restoration_plot, name = "<b> [Stats]</b> restoration hectare") +
  # tmap::tm_borders(lwd = 2, col = "red")

tmp

## Warning: The shape <b> [Seascape]</b> habitats is invalid (after reprojection).
## See sf::st_is_valid

## Warning: The shape <b> [Seascape]</b> habitats contains empty units (after
## reprojection).

## Warning: The shape <b> [Seascape]</b> probability is invalid (after
## reprojection). See sf::st_is_valid

## Warning: The shape <b> [Seascape]</b> probability contains empty units (after
## reprojection).

## Warning: The shape <b> [Particles]</b> competency is invalid (after
## reprojection). See sf::st_is_valid

## Warning: The shape <b> [Particles]</b> competency contains empty units (after
## reprojection).